formatting

[jalview.git] / src / jalview / analysis / Rna.java

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index ba18732..626e479 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -31,7 +31,8 @@ import jalview.datamodel.SequenceFeature;
 
 public class Rna
 {
-       static Hashtable<Integer, Integer> pairHash = new Hashtable();
+  static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
   /**
    * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
    * positions in "stack" vector. When a close bracket is reached, pair this
@@ -44,7 +45,8 @@ public class Rna
    * @return Array of SequenceFeature; type = RNA helix, begin is open base
    *         pair, end is close base pair
    */
-  public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
+  public static SequenceFeature[] GetBasePairs(CharSequence line)
+          throws WUSSParseException
   {
     Stack stack = new Stack();
     Vector pairs = new Vector();
@@ -69,7 +71,7 @@ public class Rna
         }
         Object temp = stack.pop();
         pairs.addElement(temp);
-        pairs.addElement(i);        
+        pairs.addElement(i);
       }
 
       i++;
@@ -83,30 +85,29 @@ public class Rna
     {
       int begin = Integer.parseInt(pairs.elementAt(p).toString());
       int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-      
-       outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
+
+      outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
               end, "");
-       //pairHash.put(begin, end);
+      // pairHash.put(begin, end);
 
     }
 
     return outPairs;
   }
-  
-  
+
   /**
    * Function to get the end position corresponding to a given start position
-   * @param indice - start position of a base pair
+   * 
+   * @param indice
+   *          - start position of a base pair
    * @return - end position of a base pair
    */
-  /*makes no sense at the moment :(
-  public int findEnd(int indice){
-         //TODO: Probably extend this to find the start to a given end?
-         //could be done by putting everything twice to the hash
-         ArrayList<Integer> pair = new ArrayList<Integer>();
-         return pairHash.get(indice);
-  }*/
-  
+  /*
+   * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
+   * Probably extend this to find the start to a given end? //could be done by
+   * putting everything twice to the hash ArrayList<Integer> pair = new
+   * ArrayList<Integer>(); return pairHash.get(indice); }
+   */
 
   /**
    * Figures out which helix each position belongs to and stores the helix
@@ -190,4 +191,3 @@ public class Rna
     }
   }
 }
-